Strain identifier

BacDive ID: 7445

Type strain: Yes

Species: Microbacterium binotii

Strain Designation: 18.76

Strain history: CIP <- 1982, Lab. Ident. Inst. Pasteur, Paris, France: strain 18.76 <- Foch Hosp., Suresnes, France, "Microbacterium sp."

NCBI tax ID(s): 462710 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7945

BacDive-ID: 7445

DSM-Number: 19164

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped, human pathogen

description: Microbacterium binotii 18.76 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from human blood.

NCBI tax id

  • NCBI tax id: 462710
  • Matching level: species

strain history

@refhistory
7945<- D. Clermont, CIP; CIP 101303
67770CIP 101303 <-- Lab. Ident. Inst. Pasteur, Paris, France; 18.76 <-- Foch Hosp., Suresnes, France.
116818CIP <- 1982, Lab. Ident. Inst. Pasteur, Paris, France: strain 18.76 <- Foch Hosp., Suresnes, France, "Microbacterium sp."

doi: 10.13145/bacdive7445.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium binotii
  • full scientific name: Microbacterium binotii Clermont et al. 2009

@ref: 7945

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium binotii

full scientific name: Microbacterium binotii Clermont et al. 2009

strain designation: 18.76

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
28983positiverod-shapedno
116818positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18329Lemon yellow (1012)10-14 daysISP 3
18329Lemon yellow (1012)10-14 daysISP 4
1832910-14 daysISP 5
18329Lemon yellow (1012)10-14 daysISP 6
18329Beige (1001)10-14 daysISP 7
116818

multicellular morphology

@refforms multicellular complexmedium name
18329noISP 3
18329noISP 4
18329noISP 5
18329noISP 6
18329noISP 7

pigmentation

  • @ref: 28983
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7945TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18329ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18329ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18329ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18329ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18329ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
34596MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
116818CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
116818CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7945positivegrowth28mesophilic
18329positiveoptimum28mesophilic
28983positivegrowth15-37
28983positiveoptimum30mesophilic
34596positivegrowth37mesophilic
67770positivegrowth28mesophilic
116818positivegrowth25-41
116818nogrowth10psychrophilic
116818nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28983aerobe
116818obligate aerobe

spore formation

  • @ref: 28983
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
28983NaClpositivegrowth0-6 %
28983NaClpositiveoptimum3 %
116818NaClpositivegrowth0-6 %
116818NaClnogrowth8 %
116818NaClnogrowth10 %

murein

  • @ref: 7945
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

@refobservation
28983aggregates in clumps
67770quinones: MK-10, MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2898322599arabinose+carbon source
2898317057cellobiose+carbon source
2898328757fructose+carbon source
2898328260galactose+carbon source
2898324265gluconate+carbon source
2898317234glucose+carbon source
2898317754glycerol+carbon source
2898317716lactose+carbon source
2898317306maltose+carbon source
2898329864mannitol+carbon source
2898337684mannose+carbon source
2898317814salicin+carbon source
2898317992sucrose+carbon source
2898327082trehalose+carbon source
2898318222xylose+carbon source
289834853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch+builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
11681816947citrate-carbon source
1168184853esculin+hydrolysis
116818606565hippurate-hydrolysis
11681817632nitrate-reduction
11681816301nitrite-reduction
11681817632nitrate+respiration
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 116818
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11681815688acetoin-
11681817234glucose+

enzymes

@refvalueactivityec
28983acid phosphatase+3.1.3.2
28983alpha-galactosidase+3.2.1.22
28983catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
116818oxidase+
116818beta-galactosidase-3.2.1.23
116818alcohol dehydrogenase-1.1.1.1
116818gelatinase-
116818amylase+
116818DNase+
116818caseinase-3.4.21.50
116818catalase+1.11.1.6
116818tween esterase+
116818gamma-glutamyltransferase-2.3.2.2
116818lecithinase-
116818lipase-
116818lysine decarboxylase-4.1.1.18
116818ornithine decarboxylase-4.1.1.17
116818phenylalanine ammonia-lyase-4.3.1.24
116818protease-
116818tryptophan deaminase-
116818urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18329++---++++--+-++++--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18329-+++++-+-++++++++--
116818-++-+----++++-+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116818+--+-+---++++----+--+/--+/-++++++-++---+--++------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116818+-+------+--------+--+-----------+-+------------+------+------------+------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7945human bloodSuresnes, Foch hospitalFranceFRAEurope
67770Human bloodSuresnesFranceFRAEurope
116818Human, BloodSuresnesFranceFRAEurope1976

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Blood

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
7945yes, in single cases1Risk group (German classification)
1168181Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7945
  • description: Microbacterium binotii strain CIP 101303 16S ribosomal RNA gene, partial sequence
  • accession: EF567306
  • length: 1406
  • database: ena
  • NCBI tax ID: 462710

GC content

@refGC-contentmethod
794571.7high performance liquid chromatography (HPLC)
2898371

External links

@ref: 7945

culture collection no.: DSM 19164, CIP 101303, NBRC 110787, JCM 16365

straininfo link

  • @ref: 76893
  • straininfo: 68086

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406785Microbacterium binotii sp. nov., isolated from human blood.Clermont D, Diard S, Bouchier C, Vivier C, Bimet F, Motreff L, Welker M, Kallow W, Bizet CInt J Syst Evol Microbiol10.1099/ijs.0.003160-02009Actinomycetales/chemistry/*classification/genetics/isolation & purification, Actinomycetales Infections/*microbiology, Bacterial Typing Techniques, Base Composition, Blood/*microbiology, DNA, Bacterial/analysis/genetics, Genes, rRNA, Genotype, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationGenetics
Phylogeny22447697Microbacterium neimengense sp. nov., isolated from the rhizosphere of maize.Gao M, Wang M, Zhang YC, Zou XL, Xie LQ, Hu HY, Xu J, Gao JL, Sun JGInt J Syst Evol Microbiol10.1099/ijs.0.038166-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis, Zea mays/*microbiologyGenetics
Phylogeny23264499Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil.Mondani L, Piette L, Christen R, Bachar D, Berthomieu C, Chapon VInt J Syst Evol Microbiol10.1099/ijs.0.048454-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, France, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, *Uranium, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7945Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19164)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19164
18329Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19164.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
28983Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2541628776041
34596Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12863
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
76893Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID68086.1StrainInfo: A central database for resolving microbial strain identifiers
116818Curators of the CIPCollection of Institut Pasteur (CIP 101303)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20101303